sommer (version 2.1)

augment: augment design example.

Description

This dataset contains phenotpic data for one trait evaluated in the experimental design known as augmented design. This model allows to obtain BLUPs for genotypes that are unreplicated by dividing the field in blocks and replicating 'check genotypes' in the blocks and unreplicated genotypes randomly within the blocks. The presence of check genotypes (usually cultivars) allows the adjustment of unreplicated genotypes.

Usage

data("augment")

Format

The format is: chr "augment"

Source

This data was generated by a potato study.

References

Covarrubias-Pazaran G (2016) Genome assisted prediction of quantitative traits using the R package sommer. PLoS ONE 11(6): doi:10.1371/journal.pone.0156744

See Also

The core function of the package mmer

Examples

####=========================================####
#### AUGMENTED DESIGN EXAMPLE
####=========================================####
data(augment)
head(augment)
####=========================================####
#### fit the mixed model and check summary
####=========================================####
mix1 <- mmer2(TSW ~ Check.Gen, random = ~ Block + Genotype:Check, data=augment)
summary(mix1)
blup <- mix1$u.hat$`Genotype:Check`
####=========================================####
#### get only the blups for unreplicated genotypes
####=========================================####
blup2 <- blup[grep("Check1",rownames(blup)),]